How do I bake a transparent shadow texture using Cycles bake?
As far as I know it's not possible to bake images with transparency in Cycles, but it's possible to figure out some workarounds, depending on what you want to achieve.

To bake a transparent shadow texture:


Set up your scene. I'll just use a simple tree in my example. Place a plane under your objects and scale it big enough to catch all the shadows.


Create a new image in the UV/Image Editor and unwrap the plane.


Create a simple diffuse material for the plane. Add an Image Texture node to the material and select the new image you just created.


In the Render Panel set Samples to a nice number (depending on your scene) and set Bake Type to Shadow.


Bake the image. You should have something like this:


Go to Compositing, select Use nodes and delete the default nodes. Then set up the nodes like this:


In the UV/Image Editor select Viewer Node from the drop down list.


Save the image as an RGBA file (*.png, *.tga - whatever you need).


Your baked transparent shadow texture is ready.